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NM_000136.3(FANCC):c.1534-5del AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 10, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000610407.4

Allele description [Variation Report for NM_000136.3(FANCC):c.1534-5del]

NM_000136.3(FANCC):c.1534-5del

Genes:
FANCC:FA complementation group C [Gene - OMIM - HGNC]
AOPEP:aminopeptidase O (putative) [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000136.3(FANCC):c.1534-5del
HGVS:
  • NC_000009.12:g.95101856del
  • NG_011707.1:g.220855del
  • NM_000136.3:c.1534-5delMANE SELECT
  • NM_001243743.2:c.1534-5del
  • LRG_497t1:c.1534-5del
  • LRG_497:g.220855del
  • NC_000009.11:g.97864137del
  • NC_000009.11:g.97864138del
  • NM_000136.2:c.1534-5del
  • NM_000136.2:c.1534-5delT
  • NM_000136.3:c.1534-5delTMANE SELECT
Links:
dbSNP: rs748342368
NCBI 1000 Genomes Browser:
rs748342368
Molecular consequence:
  • NM_000136.3:c.1534-5del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001243743.2:c.1534-5del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001363460Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Oct 10, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001363460.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: FANCC c.1534-5delT alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 4.8e-05 in 250192 control chromosomes, predominantly at a frequency of 0.00035 within the Latino subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in FANCC causing Fanconi Anemia Group C (0.00035 vs 0.0018), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.1534-5delT in individuals affected with Fanconi Anemia Group C and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submissions (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2024